Hi everyone,
we just recently got a SOLiD platform and are in the process of finding the best possible pipeline for our analysis. we are considering aligning on Bioscope 1.2, SHRiMP2 and BFAST and will probably run our analysis on the 3 of them and do a bit of comparison. is there another aligner you would recommend over those 3? and if you have been using Bioscope/SHRiMP2/BFAST which one would you recommend?
which other "after alignment" softwares would you recommand? we will use SAMtools and Picard to play around with SAM/BAM files and then use IGV for visualizing the results...
thanks in advance for your time and inputs.
Fabrice.
PS: we will start by doing some human samples whole exome using the nimblegen in-solution enrichment kit
we just recently got a SOLiD platform and are in the process of finding the best possible pipeline for our analysis. we are considering aligning on Bioscope 1.2, SHRiMP2 and BFAST and will probably run our analysis on the 3 of them and do a bit of comparison. is there another aligner you would recommend over those 3? and if you have been using Bioscope/SHRiMP2/BFAST which one would you recommend?
which other "after alignment" softwares would you recommand? we will use SAMtools and Picard to play around with SAM/BAM files and then use IGV for visualizing the results...
thanks in advance for your time and inputs.
Fabrice.
PS: we will start by doing some human samples whole exome using the nimblegen in-solution enrichment kit
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